Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computational approaches have emerged as valuable tools, leveraging physics-based-principles and machine learning to predict RNA structures rapidly.

Racial and Ethnic Underserved Populations Prescription Analgesic Use Before and After Lower Extremity Amputation in US Medicare.

Background: Racial disparities exist in access to health care and management of multiple health conditions including chronic pain; however, racial disparities in pre- and postoperative pain management in lower extremity amputation are not well-studied. Our objective was to examine the association between different racial and ethnic groups and prescription opioid and other analgesics use before and after lower extremity amputation. We hypothesize prescription opioid and other analgesic use among Black, Hispanic, and Native American US Medicare beneficiaries undergoing lower extremity amputations will be lower compared to White US Medicare beneficiaries.

Shear wave elastography of transverse carpal ligament increased with simulated carpal tunnel pressure.

Background: Elevation of carpal tunnel pressure is known to be associated with carpal tunnel syndrome. This study aimed to correlate the shear wave elastography in the transverse carpal ligament (TCL) with carpal tunnel pressures using a cadaveric model.

Methods: Eight human cadaveric hands were dissected to evacuate the tunnels.

Association between Opioid-Benzodiazepine Trajectories and Injurious Fall Risk among US Medicare Beneficiaries.

Concurrent opioid (OPI) and benzodiazepine (BZD) use may exacerbate injurious fall risk (e.g., falls and fractures) compared to no use or use alone.

Cachexia in preclinical rheumatoid arthritis: Longitudinal observational study of thigh magnetic resonance imaging from osteoarthritis initiative cohort.

Background: Preclinical rheumatoid arthritis (Pre-RA) is defined as the early stage before the development of clinical RA. While cachexia is a well-known and potentially modifiable complication of RA, it is not known if such an association exists also in the Pre-RA stage. To investigate such issue, we aimed to compare the longitudinal alterations in the muscle composition and adiposity of participants with Pre-RA with the matched controls.

N-GlycoPred: A hybrid deep learning model for accurate identification of N-glycosylation sites.

Studies have shown that protein glycosylation in cells reflects the real-time dynamics of biological processes, and the occurrence and development of many diseases are closely related to protein glycosylation. Abnormal protein glycosylation can be used as a potential diagnostic and prognostic marker of a disease, as well as a therapeutic target and a new breakthrough point for exploring pathogenesis. To address the issue of significant differences in the prediction results of previous models for different species, we constructed a hybrid deep learning model N-GlycoPred on the basis of dual-layer convolution, a paired attention mechanism and BiLSTM for accurate identification of N-glycosylation sites.

RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method.

Small molecule drugs can be used to target nucleic acids (NA) to regulate biological processes. Computational modeling methods, such as molecular docking or scoring functions, are commonly employed to facilitate drug design. However, the accuracy of the scoring function in predicting the closest-to-native docking pose is often suboptimal.

Bicycling over a Lifetime Is Associated with Less Symptomatic Knee Osteoarthritis: Data from the Osteoarthritis Initiative.

Introduction: This study aimed to evaluate the relationship between a history of bicycling and symptomatic and structural outcomes of knee osteoarthritis (OA), the most common form of arthritis.

Methods: This was a retrospective, cross-sectional study within the Osteoarthritis Initiative (OAI), where we investigated OAI participants with complete data on bicycling, knee pain, and radiographic evidence of knee OA. We used a self-administered questionnaire at the 96-month OAI visit to identify participation in bicycling during four time periods throughout a participant's lifetime (ages 12-18, 19-34, 35-49, and >50 yr).

Gardening/yardwork in people with knee osteoarthritis is not associated with symptom or structural progression over 48 months: data from the Osteoarthritis Initiative.

Objective: To evaluate the relationship of gardening/yardwork with symptomatic and structural progression in those with pre-existing radiographic knee osteoarthritis (OA) in the Osteoarthritis Initiative (OAI), an observational study designed to evaluate potential and known biomarkers and risk factors of knee OA.

Methods: We conducted a cohort study nested within the OAI, including participants ≥ 50 years old with radiographic OA in at least one knee at the time of OAI enrollment. A participant reported the level of gardening/yardwork activity in a self-administered survey.

Coccidioides Serologic Screening Practices in Individuals With Rheumatic and Autoimmune Diseases.

Objective: We aimed to estimate Coccidioides serologic screening rates before initiation of biologic disease-modifying antirheumatic drugs including tofacitinib (b/tsDMARDs), conventional synthetic disease-modifying antirheumatic drugs (csDMARDs), and/or noninhaled corticosteroids.

Methods: This retrospective cohort study used 2011 to 2016 US Medicare claims data and included beneficiaries with rheumatic or autoimmune disease residing in regions within Arizona, California, and Texas endemic for Coccidioides spp. with ≥1 prescription for a b/tsDMARD, csDMARD, and/or noninhaled corticosteroid.

Estimation of radiographic joint space of the trapeziometacarpal joint with computed tomographic validation.

Purpose: Joint space width (JSW) is a common metric used to evaluate joint structure on plain radiographs. For the hand, quantitative techniques are available for evaluation of the JSW of finger joints; however, such techniques have been difficult to establish for the trapeziometacarpal (TMC) joint. This study aimed to develop a validated method for measuring the radiographic joint space of the healthy TMC joint.

Risk of Coccidioidomycosis Infection Among Individuals Using Biologic Response Modifiers, Corticosteroids, and Oral Small Molecules.

Objective: The study objective was to examine associations between the use of biologic response modifiers (BRMs), corticosteroids, and oral small molecules (OSMs) and subsequent coccidioidomycosis infection risk among US Medicare beneficiaries with rheumatic or autoimmune diseases.

Methods: This retrospective cohort study used US 2011 to 2016 Medicare claims data. We identified geographic areas with endemic coccidioidomycosis (≥25 cases per 10,000 beneficiaries).

Strength Training Is Associated With Less Knee Osteoarthritis: Data From the Osteoarthritis Initiative.

Objective: We aimed to evaluate the relationship of a history of strength training with symptomatic and structural outcomes of knee osteoarthritis (OA).

Methods: This study was a retrospective, cross-sectional study within the Osteoarthritis Initiative (OAI), a multicenter prospective longitudinal observational study. Data were collected at four OAI clinical sites: Memorial Hospital of Rhode Island, the Ohio State University, the University of Pittsburgh, and the University of Maryland/Johns Hopkins.

2023 American College of Rheumatology and American Association of Hip and Knee Surgeons Clinical Practice Guideline for the Optimal Timing of Elective Hip or Knee Arthroplasty for Patients With Symptomatic Moderate-to-Severe Osteoarthritis or Advanced Symptomatic Osteonecrosis With Secondary Arthritis for Whom Nonoperative Therapy Is Ineffective.

Objective: To develop evidence-based consensus recommendations for the optimal timing of hip and knee arthroplasty to improve patient-important outcomes including, but not limited to, pain, function, infection, hospitalization, and death at 1 year for patients with symptomatic and radiographic moderate-to-severe osteoarthritis or advanced symptomatic osteonecrosis with secondary arthritis of the hip or knee who have previously attempted nonoperative therapy, and for whom nonoperative therapy was ineffective, and who have chosen to undergo elective hip or knee arthroplasty (collectively referred to as TJA).

Methods: We developed 13 clinically relevant population, intervention, comparator, outcomes (PICO) questions. After a systematic literature review, the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence (high, moderate, low, or very low), and evidence tables were created.

2023 American College of Rheumatology and American Association of Hip and Knee Surgeons Clinical Practice Guideline for the Optimal Timing of Elective Hip or Knee Arthroplasty for Patients With Symptomatic Moderate-to-Severe Osteoarthritis or Advanced Symptomatic Osteonecrosis With Secondary Arthritis for Whom Nonoperative Therapy Is Ineffective.

Objective: To develop evidence-based consensus recommendations for the optimal timing of hip and knee arthroplasty to improve patient-important outcomes including, but not limited to, pain, function, infection, hospitalization, and death at 1 year for patients with symptomatic and radiographic moderate-to-severe osteoarthritis or advanced symptomatic osteonecrosis with secondary arthritis of the hip or knee who have previously attempted nonoperative therapy, and for whom nonoperative therapy was ineffective, and who have chosen to undergo elective hip or knee arthroplasty (collectively referred to as TJA).

Methods: We developed 13 clinically relevant population, intervention, comparator, outcomes (PICO) questions. After a systematic literature review, the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence (high, moderate, low, or very low), and evidence tables were created.

2023 American College of Rheumatology and American Association of Hip and Knee Surgeons Clinical Practice Guideline for the Optimal Timing of Elective Hip or Knee Arthroplasty for Patients With Symptomatic Moderate-to-Severe Osteoarthritis or Advanced Symptomatic Osteonecrosis With Secondary Arthritis for Whom Nonoperative Therapy Is Ineffective.

Objective: To develop evidence-based consensus recommendations for the optimal timing of hip and knee arthroplasty to improve patient-important outcomes including, but not limited to, pain, function, infection, hospitalization, and death at 1 year for patients with symptomatic and radiographic moderate-to-severe osteoarthritis or advanced symptomatic osteonecrosis with secondary arthritis of the hip or knee who have previously attempted nonoperative therapy, and for whom nonoperative therapy was ineffective, and who have chosen to undergo elective hip or knee arthroplasty (collectively referred to as TJA).

Methods: We developed 13 clinically relevant population, intervention, comparator, outcomes (PICO) questions. After a systematic literature review, the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence (high, moderate, low, or very low), and evidence tables were created.

Self-Supervised Contrastive Representation Learning for Semi-Supervised Time-Series Classification.

Learning time-series representations when only unlabeled data or few labeled samples are available can be a challenging task. Recently, contrastive self-supervised learning has shown great improvement in extracting useful representations from unlabeled data via contrasting different augmented views of data. In this work, we propose a novel Time-Series representation learning framework via Temporal and Contextual Contrasting (TS-TCC) that learns representations from unlabeled data with contrastive learning.

Does Physical Activity Confound Race Differences in Osteoarthritis-Related Functional Limitation?

Objective: This study sought to determine the extent to which physical activity confounds the relation between race and the incidence of osteoarthritis (OA)-related functional limitation.

Methods: OA Initiative study participants with or at increased risk of knee OA who wore an accelerometer were included. Race was self-reported.

ViPal: A framework for virulence prediction of influenza viruses with prior viral knowledge using genomic sequences.

Influenza viruses pose great threats to public health and cause enormous economic losses every year. Previous work has revealed the viral factors associated with the virulence of influenza viruses in mammals. However, taking prior viral knowledge represented by heterogeneous categorical and discrete information into account to explore virus virulence is scarce in the existing work.

Reliability and Validity of Single Axial Slice vs. Multiple Slice Quantitative Measurement of the Volume of Effusion-Synovitis on 3T Knee MRI in Knees with Osteoarthritis.

Effusion-synovitis (ES) is recognized as a component of osteoarthritis, creating a need for rapid methods to assess ES on MRI. We describe the development and reliability of an efficient single-slice semi-automated quantitative approach to measure ES. We used two samples from the Osteoarthritis Initiative (OAI): 50 randomly selected OAI participants with radiographic osteoarthritis (i.

Self-supervised Learning for Label-Efficient Sleep Stage Classification: A Comprehensive Evaluation.

The past few years have witnessed a remarkable advance in deep learning for EEG-based sleep stage classification (SSC). However, the success of these models is attributed to possessing a massive amount of labeled data for training, limiting their applicability in real-world scenarios. In such scenarios, sleep labs can generate a massive amount of data, but labeling can be expensive and time-consuming.

Virulence network of interacting domains of influenza a and mouse proteins.

There exist several databases that provide virus-host protein interactions. While most provide curated records of interacting virus-host protein pairs, information on the strain-specific virulence factors or protein domains involved, is lacking. Some databases offer incomplete coverage of influenza strains because of the need to sift through vast amounts of literature (including those of major viruses including HIV and Dengue, besides others).